Interpret ImpulseDE2 output?
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Entering edit mode
5 weeks ago
CTLong ▴ 110

Hi all,

I have some uncertainties trying to interpret the FDR values from the output table of ImpulseDE2. Let's say I run the following code:

objectImpulseDE2 <- runImpulseDE2(
matCountData = lsSimulatedData$matObservedCounts,
dfAnnotation = lsSimulatedData$dfAnnotation,
boolCaseCtrl = FALSE,
vecConfounders  = c("Batch"),
boolIdentifyTransients = TRUE,
scaNProc = 1 )

This would give me an output containing the following key columns:

Gene

p

padj

loglik_full

loglik_red

impulseTOsigmoid_padj

sigmoidTOconst_padj

isTransient

isMonotonous

My question then is, if I want to use a different cutoff to select significant transient and progression genes (hence I need to filter the output based on FDR), which padj column correspond to is.Transient and is.Monotonous respectively? Also, does the output table contain information whether this gene is upregulated or downregulated? Thanks in advance.

RNA-seq • 111 views
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